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### Imports

import(BiocGenerics)
import(S4Vectors)
import(Biobase)
importClassesFrom(IRanges, NumericList)
importClassesFrom(methods, ANY, character, environment, formula, list, matrix,
                  missing, "NULL", ".NULL")
importMethodsFrom(methods, initialize, show)
importFrom(Biostrings, BStringSet, DNAStringSet)
importFrom(ggbeeswarm, position_beeswarm)
importFrom(ggiraph, geom_boxplot_interactive, geom_line_interactive,
           geom_point_interactive, GeomInteractiveBoxplot, GeomInteractiveLine,
           GeomInteractivePoint)
importFrom(ggplot2, aes, aes_, aes_string, autoplot, element_blank,
           element_text, geom_hline, ggplot, guide_legend, guides, layer,
           scale_x_continuous, scale_x_discrete, scale_y_continuous,
           stat_boxplot, theme, theme_get, rel, scale_colour_manual, 
           scale_shape_manual, element_line, unit, margin, 
           element_rect, geom_segment, scale_linetype_manual, 
           geom_text)
importFrom(grDevices, colorRampPalette)
importFrom(ggthemes, tableau_color_pal)
importFrom(IRanges, NumericList)
importFrom(methods, as, callGeneric, callNextMethod, is, validObject, new)
importFrom(pheatmap, pheatmap)
importFrom(RColorBrewer, brewer.pal)
importFrom(stats, as.formula, coef, lm, model.frame, qnorm, quantile, update,
           reorder)
importFrom(utils, read.csv, write.csv)


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### Export S4 classes

exportClasses(SignatureSet, NanoStringRccSet)

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### Export S4 generics

export("weights<-",
       NanoStringRccSet,
       sData, svarLabels, groups, "groups<-", version, "version<-",
       signatures, "signatures<-", signatureScores, signatureGroups,
       endogenousSubset, housekeepingSubset, getSigFuncs,
       negativeControlSubset, positiveControlSubset,
       controlSubset, nonControlSubset, signatureSubset,
       assayDataApply, signatureScoresApply, esBy,
       munge, signatureFuncs, "setSignatureFuncs<-", "setSignatureGroups<-",
       setQCFlags)

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### Export S4 methods

exportMethods(show,
              weights, "weights<-", length, names, lengths,
              NanoStringRccSet, groups, "groups<-", version, "version<-",
              sData, svarLabels, dimLabels, "dimLabels<-",
              signatures, "signatures<-", signatureScores,
              design, "design<-", signatureGroups,
              summary, "[", subset, "setSignatureFuncs<-", "setSignatureGroups<-",
              endogenousSubset, housekeepingSubset,
              negativeControlSubset, positiveControlSubset,
              controlSubset, nonControlSubset, signatureSubset,
              assayDataApply, signatureScoresApply, esBy, with,
              munge, transform, getSigFuncs, signatureFuncs,
              setQCFlags, normalize)

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### Export non-generic functions

export(SignatureSet,
       readNanoStringRccSet,
       readRccFile,
       readRlfFile,
       writeNanoStringRccSet,
       fThresh, fCenter, fScale,
       sThresh, sCenter, sScale,
       fIntThresh, fIntCenter, fIntScale,
       sIntThresh, sIntCenter, sIntScale,
       fAbove, fBelow, fAtLeast, fAtMost,
       sAbove, sBelow, sAtLeast, sAtMost,
       logt, log2t,
       geom_beeswarm_interactive, update_geom_params)

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### Export S3 methods

S3method(ggplot, NanoStringRccSet)
S3method(autoplot, NanoStringRccSet)
